Imputation Report For Cohort: tmp

Per chromosome imputation report for cohort tmp.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 1.4.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 35589570 88.190
0.1 1219755 3.023
0.2 810372 2.008
0.3 620059 1.536
0.4 497543 1.233
0.5 408867 1.013
0.6 347624 0.861
0.7 293583 0.727
0.8 247936 0.614
0.9 320380 0.794
1.0 23 0.000
Total 40355712 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.0 27433132 67.978
0.1 720559 1.786
0.2 396639 0.983
0.3 320114 0.793
0.4 341848 0.847
0.5 430733 1.067
0.6 657402 1.629
0.7 1041614 2.581
0.8 1756496 4.353
0.9 7228707 17.912
1.0 28468 0.071
Total 40355712 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2713439 88.3876
0.1 89996 2.9315
0.2 57477 1.8723
0.3 46013 1.4988
0.4 37698 1.2280
0.5 30435 0.9914
0.6 27340 0.8906
0.7 21879 0.7127
0.8 18796 0.6123
0.9 26857 0.8748
1.0 1 0.0000
Total 3069931

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 2093396 68.1903
0.1 55491 1.8076
0.2 30704 1.0002
0.3 25267 0.8230
0.4 26183 0.8529
0.5 33281 1.0841
0.6 50587 1.6478
0.7 80200 2.6124
0.8 134554 4.3830
0.9 538310 17.5349
1.0 1958 0.0638
Total 3069931

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 3004239 88.5622
0.1 101701 2.9981
0.2 64633 1.9053
0.3 50361 1.4846
0.4 38270 1.1282
0.5 32132 0.9472
0.6 29087 0.8575
0.7 22829 0.6730
0.8 21184 0.6245
0.9 27801 0.8195
Total 3392237

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 2328590 68.6447
0.1 59126 1.7430
0.2 31830 0.9383
0.3 25533 0.7527
0.4 27552 0.8122
0.5 33386 0.9842
0.6 50931 1.5014
0.7 82426 2.4298
0.8 141643 4.1755
0.9 608970 17.9519
1.0 2250 0.0663
Total 3392237

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2489338 88.2151
0.1 87376 3.0964
0.2 56248 1.9933
0.3 42531 1.5072
0.4 34736 1.2309
0.5 29219 1.0354
0.6 24751 0.8771
0.7 20377 0.7221
0.8 16803 0.5955
0.9 20514 0.7270
1.0 1 0.0000
Total 2821894

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1919954 68.0378
0.1 48409 1.7155
0.2 26776 0.9489
0.3 21548 0.7636
0.4 22678 0.8036
0.5 28252 1.0012
0.6 43574 1.5441
0.7 70686 2.5049
0.8 119655 4.2402
0.9 518045 18.3581
1.0 2317 0.0821
Total 2821894

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2444008 87.6749
0.1 81445 2.9217
0.2 60234 2.1608
0.3 45786 1.6425
0.4 33643 1.2069
0.5 27624 0.9910
0.6 25015 0.8974
0.7 21948 0.7873
0.8 20060 0.7196
0.9 27817 0.9979
1.0 1 0.0000
Total 2787581

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1885554 67.6412
0.1 47341 1.6983
0.2 25567 0.9172
0.3 20650 0.7408
0.4 22170 0.7953
0.5 27962 1.0031
0.6 42240 1.5153
0.7 69175 2.4815
0.8 119958 4.3033
0.9 525348 18.8460
1.0 1616 0.0580
Total 2787581

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2290759 88.5089
0.1 76342 2.9497
0.2 52147 2.0148
0.3 40114 1.5499
0.4 31572 1.2199
0.5 24954 0.9642
0.6 22188 0.8573
0.7 18512 0.7153
0.8 15383 0.5944
0.9 16196 0.6258
1.0 1 0.0000
Total 2588168

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1763151 68.1235
0.1 43688 1.6880
0.2 24252 0.9370
0.3 19406 0.7498
0.4 20460 0.7905
0.5 25511 0.9857
0.6 39307 1.5187
0.7 63248 2.4437
0.8 108111 4.1771
0.9 478855 18.5017
1.0 2179 0.0842
Total 2588168

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2156804 87.6710
0.1 79488 3.2311
0.2 52857 2.1486
0.3 40821 1.6593
0.4 32773 1.3322
0.5 26436 1.0746
0.6 21956 0.8925
0.7 17809 0.7239
0.8 15115 0.6144
0.9 16052 0.6525
Total 2460111

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1645996 66.9074
0.1 40353 1.6403
0.2 22237 0.9039
0.3 17817 0.7242
0.4 18604 0.7562
0.5 22926 0.9319
0.6 35135 1.4282
0.7 56156 2.2827
0.8 96860 3.9372
0.9 499269 20.2946
1.0 4758 0.1934
Total 2460111

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2019910 88.2325
0.1 68609 2.9969
0.2 48590 2.1225
0.3 35253 1.5399
0.4 29755 1.2997
0.5 23670 1.0339
0.6 18935 0.8271
0.7 15953 0.6968
0.8 12645 0.5524
0.9 15985 0.6982
Total 2289305

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1560178 68.1507
0.1 41044 1.7929
0.2 23169 1.0121
0.3 17750 0.7753
0.4 18555 0.8105
0.5 23518 1.0273
0.6 36492 1.5940
0.7 58533 2.5568
0.8 98326 4.2950
0.9 410592 17.9352
1.0 1148 0.0501
Total 2289305

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1988197 88.6517
0.1 64892 2.8935
0.2 44885 2.0014
0.3 31968 1.4254
0.4 27683 1.2344
0.5 22656 1.0102
0.6 18442 0.8223
0.7 15889 0.7085
0.8 13458 0.6001
0.9 14635 0.6526
Total 2242705

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1540133 68.6730
0.1 37510 1.6725
0.2 21215 0.9460
0.3 16828 0.7503
0.4 18293 0.8157
0.5 22422 0.9998
0.6 33323 1.4858
0.7 54054 2.4102
0.8 91390 4.0750
0.9 405713 18.0903
1.0 1824 0.0813
Total 2242705

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1487517 88.2029
0.1 55269 3.2772
0.2 32574 1.9315
0.3 25271 1.4985
0.4 20587 1.2207
0.5 16220 0.9618
0.6 14551 0.8628
0.7 11891 0.7051
0.8 9962 0.5907
0.9 12627 0.7487
1.0 2 0.0001
Total 1686471

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1137244 67.4334
0.1 31517 1.8688
0.2 16930 1.0039
0.3 13605 0.8067
0.4 14186 0.8412
0.5 17392 1.0313
0.6 27816 1.6494
0.7 45022 2.6696
0.8 75939 4.5028
0.9 306144 18.1529
1.0 676 0.0401
Total 1686471

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1692555 87.8108
0.1 60105 3.1183
0.2 40193 2.0852
0.3 28434 1.4752
0.4 25344 1.3149
0.5 20777 1.0779
0.6 16672 0.8650
0.7 14264 0.7400
0.8 12814 0.6648
0.9 16344 0.8479
1.0 1 0.0001
Total 1927503

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1301616 67.5286
0.1 32472 1.6847
0.2 17956 0.9316
0.3 14207 0.7371
0.4 15288 0.7932
0.5 19002 0.9858
0.6 28722 1.4901
0.7 47390 2.4586
0.8 84387 4.3780
0.9 365335 18.9538
1.0 1128 0.0585
Total 1927503

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1702069 87.8719
0.1 57685 2.9781
0.2 36583 1.8887
0.3 31054 1.6032
0.4 24637 1.2719
0.5 20528 1.0598
0.6 18377 0.9487
0.7 14192 0.7327
0.8 12609 0.6510
0.9 19256 0.9941
Total 1936990

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1308707 67.5640
0.1 34157 1.7634
0.2 18083 0.9336
0.3 14254 0.7359
0.4 14474 0.7472
0.5 17910 0.9246
0.6 29248 1.5100
0.7 49485 2.5547
0.8 84042 4.3388
0.9 364855 18.8362
1.0 1775 0.0916
Total 1936990

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1626923 88.0314
0.1 55740 3.0160
0.2 35699 1.9316
0.3 29810 1.6130
0.4 24035 1.3005
0.5 18940 1.0248
0.6 15692 0.8491
0.7 12677 0.6859
0.8 12900 0.6980
0.9 15696 0.8493
1.0 5 0.0003
Total 1848117

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 1249720 67.6213
0.1 32282 1.7468
0.2 17691 0.9572
0.3 14334 0.7756
0.4 15346 0.8304
0.5 19310 1.0448
0.6 29235 1.5819
0.7 47689 2.5804
0.8 81509 4.4104
0.9 339832 18.3880
1.0 1169 0.0633
Total 1848117

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1206984 87.1196
0.1 42966 3.1013
0.2 28142 2.0313
0.3 22842 1.6487
0.4 17215 1.2426
0.5 15864 1.1451
0.6 12687 0.9157
0.7 11376 0.8211
0.8 9670 0.6980
0.9 17686 1.2766
1.0 1 0.0001
Total 1385433

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 925753 66.8205
0.1 25070 1.8095
0.2 13384 0.9661
0.3 10674 0.7704
0.4 11299 0.8156
0.5 13981 1.0091
0.6 21928 1.5828
0.7 36318 2.6214
0.8 60109 4.3386
0.9 265833 19.1877
1.0 1084 0.0782
Total 1385433

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1116023 88.1162
0.1 39784 3.1412
0.2 26249 2.0725
0.3 18521 1.4623
0.4 15590 1.2309
0.5 11852 0.9358
0.6 10050 0.7935
0.7 9632 0.7605
0.8 7841 0.6191
0.9 10993 0.8680
1.0 1 0.0001
Total 1266536

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 862465 68.0964
0.1 23350 1.8436
0.2 12276 0.9693
0.3 9650 0.7619
0.4 10028 0.7918
0.5 12792 1.0100
0.6 19932 1.5737
0.7 31321 2.4730
0.8 53774 4.2458
0.9 230275 18.1815
1.0 673 0.0531
Total 1266536

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1005863 88.2944
0.1 32460 2.8493
0.2 22861 2.0067
0.3 17342 1.5223
0.4 13770 1.2087
0.5 11908 1.0453
0.6 8903 0.7815
0.7 7870 0.6908
0.8 6877 0.6037
0.9 11359 0.9971
1.0 2 0.0002
Total 1139215

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 779005 68.3809
0.1 21279 1.8679
0.2 11934 1.0476
0.3 9749 0.8558
0.4 10930 0.9594
0.5 13990 1.2280
0.6 20558 1.8046
0.7 30945 2.7163
0.8 51359 4.5083
0.9 188979 16.5885
1.0 487 0.0427
Total 1139215

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1139593 88.9406
0.1 37393 2.9184
0.2 22965 1.7923
0.3 18971 1.4806
0.4 14277 1.1143
0.5 12395 0.9674
0.6 10630 0.8296
0.7 9436 0.7364
0.8 6874 0.5365
0.9 8763 0.6839
Total 1281297

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 888172 69.3182
0.1 24011 1.8740
0.2 12732 0.9937
0.3 10183 0.7947
0.4 11339 0.8850
0.5 14191 1.1075
0.6 23118 1.8043
0.7 36692 2.8637
0.8 61907 4.8316
0.9 198615 15.5011
1.0 337 0.0263
Total 1281297

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 966744 88.6863
0.1 30561 2.8036
0.2 22907 2.1014
0.3 15799 1.4494
0.4 13001 1.1927
0.5 11413 1.0470
0.6 8981 0.8239
0.7 8030 0.7366
0.8 5856 0.5372
0.9 6780 0.6220
Total 1090072

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 748320 68.6487
0.1 22920 2.1026
0.2 12621 1.1578
0.3 10155 0.9316
0.4 11530 1.0577
0.5 15390 1.4118
0.6 22059 2.0236
0.7 33038 3.0308
0.8 51731 4.7456
0.9 161909 14.8531
1.0 399 0.0366
Total 1090072

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 968676 87.6824
0.1 34193 3.0951
0.2 23589 2.1352
0.3 17549 1.5885
0.4 13971 1.2646
0.5 11147 1.0090
0.6 8972 0.8121
0.7 8474 0.7670
0.8 6792 0.6148
0.9 11387 1.0307
1.0 5 0.0005
Total 1104755

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 745594 67.4895
0.1 20600 1.8647
0.2 11417 1.0334
0.3 9571 0.8663
0.4 9761 0.8835
0.5 13373 1.2105
0.6 20192 1.8277
0.7 30612 2.7709
0.8 51902 4.6981
0.9 191291 17.3152
1.0 442 0.0400
Total 1104755

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 766424 88.2414
0.1 29178 3.3594
0.2 19009 2.1886
0.3 13015 1.4985
0.4 9662 1.1124
0.5 8987 1.0347
0.6 6983 0.8040
0.7 5996 0.6903
0.8 4707 0.5419
0.9 4593 0.5288
Total 868554

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 590519 67.9887
0.1 16000 1.8421
0.2 9502 1.0940
0.3 7931 0.9131
0.4 9298 1.0705
0.5 12534 1.4431
0.6 18814 2.1661
0.7 27945 3.2174
0.8 43966 5.0620
0.9 131590 15.1505
1.0 455 0.0524
Total 868554

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 783418 88.5235
0.1 27416 3.0979
0.2 17765 2.0074
0.3 13663 1.5439
0.4 11044 1.2479
0.5 8826 0.9973
0.6 7642 0.8635
0.7 5930 0.6701
0.8 4673 0.5280
0.9 4606 0.5205
Total 884983

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 601536 67.9715
0.1 15868 1.7930
0.2 8898 1.0054
0.3 7358 0.8314
0.4 7701 0.8702
0.5 10542 1.1912
0.6 16387 1.8517
0.7 25260 2.8543
0.8 41643 4.7055
0.9 149500 16.8930
1.0 290 0.0328
Total 884983

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 466276 87.7653
0.1 16012 3.0139
0.2 10652 2.0050
0.3 8708 1.6391
0.4 7474 1.4068
0.5 6016 1.1324
0.6 4966 0.9347
0.7 4668 0.8786
0.8 3959 0.7452
0.9 2545 0.4790
Total 531276

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 362103 68.1572
0.1 10069 1.8952
0.2 5561 1.0467
0.3 4467 0.8408
0.4 4603 0.8664
0.5 6457 1.2154
0.6 9976 1.8777
0.7 14883 2.8014
0.8 24889 4.6848
0.9 88082 16.5793
1.0 186 0.0350
Total 531276

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 463772 88.4143
0.1 16097 3.0688
0.2 11034 2.1035
0.3 8370 1.5957
0.4 6865 1.3088
0.5 5467 1.0422
0.6 4603 0.8775
0.7 3909 0.7452
0.8 2695 0.5138
0.9 1732 0.3302
Total 524544

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 356493 67.9625
0.1 10897 2.0774
0.2 6318 1.2045
0.3 5029 0.9587
0.4 5451 1.0392
0.5 6853 1.3065
0.6 11016 2.1001
0.7 15837 3.0192
0.8 25721 4.9035
0.9 80781 15.4002
1.0 148 0.0282
Total 524544

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1090039 88.7629
0.1 35047 2.8539
0.2 23079 1.8793
0.3 17863 1.4546
0.4 13941 1.1352
0.5 11401 0.9284
0.6 10201 0.8307
0.7 10042 0.8177
0.8 6263 0.5100
0.9 10156 0.8270
1.0 2 0.0002
Total 1228034

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 838933 68.3151
0.1 27105 2.2072
0.2 15586 1.2692
0.3 14148 1.1521
0.4 16119 1.3126
0.5 19758 1.6089
0.6 26812 2.1833
0.7 34699 2.8256
0.8 53121 4.3257
0.9 180584 14.7051
1.0 1169 0.0952
Total 1228034

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering